4 Bin quality

load("data/data.Rdata")
#Generate quality biplot
bin_metadata %>%
  select(genome,completeness,contamination,overall_strategy, assembly, size) %>%
  ggplot(aes(x=completeness,y=contamination,size=size,color=overall_strategy)) +
              geom_point(alpha=0.3, size=1.5) +
              scale_color_manual(values=strategy_colors)+
              ylim(c(10,0)) +
              labs(y= "Contamination", x = "Completeness") +
              theme_classic() +
              theme(legend.position = "none")

bin_metadata %>%
  select(genome,completeness,contamination,overall_strategy, assembly, size) %>%
  mutate(assembly=factor(assembly,levels=assemblies)) %>%
  ggplot(aes(y=completeness,x=overall_strategy, group=overall_strategy, color=overall_strategy)) +
      geom_jitter(alpha=0.1)+
      geom_boxplot(outlier.shape = NA)+
              scale_color_manual(values=strategy_colors)+
              facet_grid(~assembly, space = "free", scale="free")+
              labs(x = "Strategies", y="Completeness") +
              theme_classic() +
              theme(legend.position = "none")

bin_metadata %>%
  select(genome,completeness,contamination,overall_strategy, assembly, size) %>%
  ggplot(aes(x=completeness,color=assembly)) +
              geom_density(alpha=0.3, size=1.5, linewidth=1) +
              scale_color_manual(values=assembly_colors)+
              labs(x = "Completeness", y="Density") +
              theme_classic()

bin_metadata %>%
  select(genome,completeness,contamination,overall_strategy, assembly, size) %>%
  mutate(assembly=factor(assembly,levels=assemblies)) %>%
  ggplot(aes(y=contamination,x=overall_strategy, group=overall_strategy, color=overall_strategy)) +
      geom_jitter(alpha=0.1)+
      geom_boxplot(outlier.shape = NA)+
              scale_color_manual(values=strategy_colors)+
              facet_grid(~assembly, space = "free", scale="free")+
              labs(x = "Strategies", y="Contamination") +
              theme_classic() +
              theme(legend.position = "none")

bin_metadata %>%
  select(genome,completeness,contamination,assembly, size) %>%
  ggplot(aes(x=contamination,color=assembly,)) +
              geom_density(alpha=0.3, size=1.5, linewidth=1) +
              scale_color_manual(values=assembly_colors)+
              labs(x = "Contamination", y="Density") +
              theme_classic()